A mobile agent is a small piece of program that migrates automatically among different platforms, on which it executes assigned tasks. Mobile agents migrate in malicious and unsecure networks. So, there will be chances of compromising mobile agent as well as host computer. So, during the mobile agent executing life cycle there will be chances of stealing of confidential information about host and agents. The application of mobile agents is increasing day by day in various domains such as distributed computing, cloud computing and Internet of Things. In this article, we propose a method based on lattice-based dynamic threshold Chinese Remainder Theorem for the security of mobile agents. The combination of dynamic threshold, lattice-based encryption-decryption and Chinese remainder theorem provides optimal security as compared to traditional approach. After the analysis of turnaround time of creation of share, distribution and recreation of secret is optimal as compared to traditional approach. Another comparison is also done on the basis of memory utilization, computational cost, communication overhead and scalability of proposed method. Proposed approaches provide effectiveness of security for mobile agents in a decentralized and malicious environment. The framework was implemented in Python and analyzed with 10 to 1000 mobile agents. With 1000 mobile agents, the framework gains a turnaround time of 12.4 ms, memory utilization of 18.7 MB, and CPU efficiency of 91.3%, demonstrating better scalability and computational cost compared with Shamir Secret Sharing, Integer CRT, Homomorphic Encryption, Vectorized Tree Parity Machine and Boneh Goh Nissim techniques. Performance evaluation based on computational cost, communication overhead and scalability further shows the effectiveness of the framework. These outcomes show that the proposed methods provide an efficient, scalable and post-quantum-secure method for securing mobile agents in cloud computing, Internet of Things (IoT), and other decentralized distributed computing environments.